Quick Start

This guide walks you through the simplest use case: comparing two bacterial genomes.

Prepare Input Files

Create two FASTA files (or use your own). For example:

cat > ecoli_k12.fasta << 'EOF'
>Escherichia_coli_K12_MG1655
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAG
TGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATT
GACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAA
EOF

cat > ecoli_o157.fasta << 'EOF'
>Escherichia_coli_O157_H7
GGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAG
TGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATT
GACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATCCCC
EOF

Run Example

fracsim -i ecoli_k12.fasta ecoli_o157.fasta --ani -k 31 -s 0.001 -V